Strain identifier

BacDive ID: 16427

Type strain: Yes

Species: Streptomyces hainanensis

Strain history: C.-L. Jiang YIM 47672.

NCBI tax ID(s): 402648 (species)

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General

@ref: 10655

BacDive-ID: 16427

DSM-Number: 41900

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, rod-shaped

description: Streptomyces hainanensis DSM 41900 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 402648
  • Matching level: species

strain history

@refhistory
10655<- J. Wiese, IFM Geomar, Kiel <- Y. Jiang
67770C.-L. Jiang YIM 47672.

doi: 10.13145/bacdive16427.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces hainanensis
  • full scientific name: Streptomyces hainanensis Jiang et al. 2007

@ref: 10655

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces hainanensis

full scientific name: Streptomyces hainanensis Jiang et al. 2007

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
320860.85 µm0.5 µmrod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19825Sepia brown10-14 daysISP 2
19825Chestnut brown10-14 daysISP 3
19825Cream10-14 daysISP 4
19825Clay brown10-14 daysISP 5
19825Beige10-14 daysISP 6
19825Cream10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19825yesAerial MyceliumCreamISP 2
19825yesAerial MyceliumCreamISP 3
19825yesAerial MyceliumCreamISP 4
19825noISP 5
19825noISP 6
19825noISP 7

pigmentation

  • @ref: 32086
  • production: yes

multimedia

  • @ref: 10655
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41900.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10655GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19825ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19825ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19825ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19825ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19825ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19825ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
10655positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32086positivegrowth06-09alkaliphile
32086positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32086
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32086yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
32086NaClpositivegrowth0-10 %
32086NaClpositiveoptimum5 %

observation

@refobservation
32086aggregates in chains
67770quinones: MK-9(H4), MK-10(H0), MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1982517234glucose+
1982522599arabinose-
1982517992sucrose+
1982518222xylose+/-
1982517268myo-inositol+/-
1982529864mannitol+
1982528757fructose+
1982526546rhamnose+
1982516634raffinose+
1982562968cellulose+
3208617057cellobiose+carbon source
3208617234glucose+carbon source
3208627082trehalose+carbon source
3208616199urea+carbon source
320864853esculin+hydrolysis
3208617632nitrate+reduction

metabolite production

  • @ref: 32086
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
32086urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19825+++-++---++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10655soil sampleHainan provinceChinaCHNAsia
67770Soil from a forest of evergreen broadleaved trees on Wuzhi MountainHainan ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_27714.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_1457;97_14887;98_18419;99_27714&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AM398645
  • Sequence Identity:
  • Total samples: 60
  • soil counts: 22
  • aquatic counts: 2
  • animal counts: 8
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
106551Risk group (German classification)
198251Risk group (German classification)

Sequence information

16S sequences

  • @ref: 10655
  • description: Streptomyces hainanensis partial 16S rRNA gene, type strain YIM 47672T
  • accession: AM398645
  • length: 1456
  • database: ena
  • NCBI tax ID: 402648

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces hainanensis strain DSM 41900402648.3wgspatric402648
66792Streptomyces hainanensis DSM 419002866725952draftimg402648
67770Streptomyces hainanensis DSM 41900GCA_004348415contigncbi402648

GC content

@refGC-contentmethod
1065573.4
6777073.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.344no
anaerobicno99.049no
halophileno80.338no
spore-formingyes94.513yes
glucose-utilyes89.451no
aerobicyes94.713no
flagellatedno98.369yes
thermophileno97.217no
motileno94.546yes
glucose-fermentno91.954no

External links

@ref: 10655

culture collection no.: DSM 41900, YIM 47672, CCTCC AA 205017, JCM 15129

straininfo link

  • @ref: 85468
  • straininfo: 294144

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978242Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces.Jiang Y, Tang SK, Wiese J, Xu LH, Imhoff JF, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64940-02007Bacterial Typing Techniques, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny18984700Streptomyces specialis sp. nov.Kampfer P, Huber B, Buczolits S, Thummes K, Grun-Wollny I, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.2008/001008-02008Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny19502341Streptomyces sedi sp. nov., isolated from surface-sterilized roots of Sedum sp.Li J, Zhao GZ, Qin S, Zhu WY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.007534-02009Bacterial Typing Techniques, Base Composition, China, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sedum/*microbiology, Sequence Analysis, DNA, Species Specificity, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny19625443Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana.Xiao J, Wang Y, Luo Y, Xie SJ, Ruan JS, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.009357-02009Avicennia/*microbiology, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/chemistry/classification/genetics/*isolation & purificationGenetics
Phylogeny24243968Streptomyces hoynatensis sp. nov., isolated from deep marine sediment.Veyisoglu A, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.055640-02013Bacterial Typing Techniques, Black Sea, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics, Turkey, Vitamin K 2/chemistry, *Water MicrobiologyGenetics
Phylogeny25237147Streptomyces burgazadensis sp. nov., isolated from soil.Saricaoglu S, Isik K, Veyisoglu A, Saygin H, Cetin D, Guven K, Sproer C, Klenk HP, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.065870-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Turkey, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
10655Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41900
19825Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41900.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32086Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85468Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294144.1StrainInfo: A central database for resolving microbial strain identifiers